Variable polarity cold metal transfer (VPCMT) is a newly developed welding process and has drawn extensive interests because of its potential in further reducing the heat input, offering greater gap bridging ability, and improving the deposition rate. Using 6061 aluminum alloy as an example, this paper systematically investigated the influences of the key parameter in VPCMT, i.e., “positive/negative electrodes ratio (EP/EN Balance),” on weld formation, microstructure, and mechanical properties. It was found that, with the increase of the EP/EN Balance value, the duty cycle of the negative phase was reduced but the peak current and maximum temperature of the weld pool were both increased resulting in a higher heat input. The positive/negative electrode ratio had little impact on the grain misorientation angle in the fusion zone. Hardness of the joint was higher with larger positive duty cycles because of the precipitate phase and small grain size. An increased negative duty cycle resulted in lower heat input leading to insufficient melting of the material and deterioration of the mechanical strength of the welds.